Gah I have a new problem now! I have dled a few clothing/armor mods to try them out. Everything works fine but when I cast invisibility or chameleon my clothes will disappear! This only happens with the mod clothes not the modded vanilla clothes.

Tried searching but didn't find anything. Anyone got any idea whats wrong/how to fix this?

Firstly does your modded clothes are still invisible when you character lost it's return visible or not ?
If yes then they should return to normal by removing them and don them again.
If no then it a common bug who happen very often by overlapping two alpha channels ( an Morrowind-object property who allow an object to turn entierly or partly transparent) its the same bug as some moded clothes disappear when the player is underwater.Unfortunaly its an game engine limitation, not a bug.however this affect only the player apparence and had no impact on the game mechanics.